Systems and methods for performing amplicon rescue multiplex polymerase chain reaction (PCR)

ABSTRACT

Embodiments of the present disclosure generally pertain to systems and methods for performing amplicon rescue multiplex polymerase chain reaction (arm-PCR). In one embodiment, the system comprises a processor and a reader coupled to a control element. The control element is configured to control the operation of the processor and the reader based on a variety of settings. The processor is configured to receive a self-contained cassette for performing PCR amplification of DNA and/or RNA obtained from an organic specimen. The processor engages with the cassette and manipulates reagents within the cassette in order to amplify and detect the DNA from the specimen. The processor also causes the cassette to deposit the DNA on a microarray within the cassette. The reader is configured to receive the cassette after it has been processed by the processor and to capture an image of the microarray for transmission to the control element as test data. The control element is further configured to analyze the test data received from the reader and to produce an output indicative of a comparison of the test data to predefined data.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.16/210,983 entitled “Systems and Methods for Performing Amplicon RescueMultiplex Polymerase Chain reaction (PCR)”, filed on Dec. 5, 2018, andgranted as U.S. Pat. No. 10,900,981, which is incorporated herein byreference. U.S. patent application Ser. No. 16/210,983 is a continuationof U.S. patent application Ser. No. 14/552,181, entitled “Systems andMethods for Performing Amplicon Rescue Multiplex Polymerase Chainreaction (PCR)”, filed on Nov. 24, 2014, and granted as U.S. Pat. No.10,345,320, which is incorporated herein by reference. U.S. patentapplication Ser. No. 14/552,181 is a continuation of and claims priorityto U.S. Patent application Ser. No. 13/674,858, entitled “Systems andMethods for Performing Amplicon Rescue Multiplex Polymerase Chainreaction (PCR)”, filed on Nov. 12, 2012, and granted as U.S. Pat. No.8,911,949, which is incorporated herein by reference. U.S. patentapplication Ser. No. 13/674,858 claims priority to U.S. ProvisionalPatent Application No. 61/558,791, entitled “Systems and Methods forPerforming Amplicon Rescue Multiplex Polymerase Chain Reaction” andfiled on Nov. 11, 2011, which is incorporated herein by reference. U.S.patent application Ser. No. 13/674,858 also claims priority to U.S.Provisional Patent Application No. 61/592,372, entitled “Systems andMethods for Performing Amplicon Rescue Multiplex Polymerase ChainReaction (PCR),” and filed on Jan. 30, 2012, which is incorporatedherein by reference.

RELATED ART

The development of the polymerase chain reaction (PCR) enables the useof DNA amplification for a variety of uses, including moleculardiagnostic testing. However, there are challenges associated with theuse of PCR for molecular differential diagnostic (MDD) assays. PCRutilizes specific primers or primer sets, temperature conditions, andenzymes. PCR reactions may easily be contaminated, primer binding mayrequire different conditions for different primers, primers should bespecific for a target sequence in order to amplify only that targetsequence, etc. This has made it even more difficult to amplify multiplesequences from a single sample.

Diagnostic testing of clinical samples to find one or more causativedisease agents has, in the past, required that microorganisms beisolated and cultured. However, this may take days while in many cases adiagnosis must be acted upon within hours if the patient's life is to besaved. Identification of one or more disease-causing agents within aclinical sample within a matter of hours is the goal, and methods havebeen developed to better accomplish that goal. For example, multiplexPCR and target-enriched multiplex PCR (tem-PCR) techniques have beendeveloped to amplify multiple nucleic acids within a sample in order toproduce enough DNA/RNA to enable detection and identification ofmultiple organisms. Mutliplex and tem-PCR techniques offer the abilityto perform multiple assays at a time on a single sample, but they mustdo so by sacrificing much of the sensitivity that can be achieved bysingle amplification reactions using a single set of target-specificprimers. It is still desirable to improve upon the technology in orderto provide diagnostic tests with greater sensitivity and shorterdiagnostic time. It is also desirable to integrate the amplification anddetection steps so that open-tube hybridization steps can be eliminatedto reduce false positives caused by carry-over contamination by PCRproducts.

BRIEF DESCRIPTION OF THE DRAWINGS

The disclosure can be better understood with reference to the followingdrawings. The elements of the drawings are not necessarily to scalerelative to each other, emphasis instead being placed upon clearlyillustrating the principles of the disclosure. Furthermore, likereference numerals designate corresponding parts throughout the severalviews.

FIG. 1 is a block diagram illustrating an exemplary system forperforming PCR amplification in accordance with the present disclosure.

FIG. 2 is a block diagram illustrating an exemplary embodiment of acontrol element, such as is depicted by FIG. 1 .

FIG. 3 is a side plan view of an exemplary processor module.

FIG. 4 is a rear perspective view of the processor module of FIG. 3 .

FIG. 5 is a partially exploded view of a heater assembly, such as isdepicted by

FIG. 3 .

FIG. 6 is a perspective view of an exemplary heater, such as is depictedby FIG. 3 .

FIG. 7 is a perspective view of a lifter assembly, such as is depictedby FIG. 3 .

FIG. 8 is a perspective view of an exemplary cam bar shaft, such as isdepicted by

FIG. 3 .

FIG. 9 is a perspective view of an exemplary plunger, such as isdepicted by FIG. 3 .

FIG. 10 is a perspective view of an exemplary lead screw shaft, such asis depicted by FIG. 3 .

FIG. 11 depicts a heater of the heater assembly of FIG. 3 engaged with acassette.

FIG. 12 is a perspective view of an exemplary embodiment of a reader,such as is depicted by FIG. 1 .

FIG. 13 is a perspective view of the reader of FIG. 12 with the driveassembly removed.

FIG. 14 is a perspective view of the reader of FIG. 12 with the driveassembly and the flywheel assembly removed.

FIG. 15 is a partially exploded view of the drive assembly of FIG. 12 .

FIG. 16 is a perspective view of the flywheel assembly of FIG. 12 .

FIG. 17 is a top perspective view of the flywheel of FIG. 12 .

FIG. 18 is a bottom perspective view of the flywheel of FIG. 17 .

FIG. 19 is a perspective view of the optics assembly of FIG. 12 .

FIG. 20 is top plan view of an exemplary embodiment of a microarray.

FIG. 21 is an exploded view of the optical cube assembly of FIG. 19 .

FIG. 22 is a block diagram depicting an exemplary open platform targetsolution system in accordance with the present disclosure.

FIG. 23 depicts a portion of a microarray image showing an exemplarydot.

FIG. 24 depicts a portion of a microarray image showing a repositionedexemplary dot.

FIG. 25 is a side cut-out view of the flywheel housing comprising abalancing weight.

FIG. 26 is an additional side cut-out view of the flywheel housing.

FIG. 27A is a back view of the balancing weight.

FIG. 27B is a side view of the balancing weight comprising two piniongears.

FIG. 27C is a side view of the balancing weight comprising one piniongear.

FIG. 28 depicts an exemplary embodiment of a cassette.

FIG. 29 depicts an exploded view of the exemplary cassette depicted byFIG. 28 .

DETAILED DESCRIPTION

Embodiments of the present disclosure generally pertain to systems andmethods for performing amplicon rescue multiplex polymerase chainreaction (arm-PCR). In one embodiment, the system comprises a processorand a reader coupled to a control element. The control element isconfigured to control the operation of the processor and the readerbased on a variety of settings. The processor is configured to receive aself-contained cassette for performing PCR amplification of DNA and/orRNA obtained from an organic specimen. The processor engages with thecassette and manipulates reagents within the cassette in order toamplify and detect the DNA from the specimen. The processor also causesthe cassette to deposit the DNA on a microarray within the cassette. Thereader is configured to receive the cassette after it has been processedby the processor and to capture an image of the microarray fortransmission to the control element as test data. The control element isfurther configured to analyze the test data received from the reader andto produce an output indicative of a comparison of the test data topredefined data.

FIG. 1 depicts an exemplary system 10 for performing PCR amplificationof DNA and/or RNA obtained from an organic specimen. The system 10enables the performance of arm-PCR, a technique that has been describedpreviously in U.S. Pat. No. 7,999,092, entitled “Amplicon RescueMultiplex Polymerase Chain Reaction for Amplication of MultipleTargets,” which is incorporated herein by reference. The system 10comprises a processor 12 and a reader 14 coupled to a control element15. In one embodiment, the control element 15 comprises a computingdevice, such as, for example, a computer, although other types ofcontrol elements 15 are possible in other embodiments. The controlelement 15 is configured to communicate with the processor 12 and thereader 14 in order to control the operation of the processor 12 and thereader 14 based on a variety of settings, discussed in more detailhereafter. The control element 15 is further configured to receive dataindicative of the specimen's amplified DNA from the reader 14 and toproduce an output indicating a comparison of the amplified DNA topredefined data, discussed in more detail hereafter. Such comparison isused in diagnosing the specimen.

The processor 12 is configured to receive a self-contained cassette 17containing the organic specimen, to engage with the cassette 17, and tomanipulate the cassette 17 such that arm-PCR is performed on thespecimen within the cassette 17. An exemplary cassette is disclosed inU.S. Pat. No. 8,383,068, entitled “Apparatus for Performing AmpliconRescue Multiplex PCR,” which is incorporated herein by reference. In oneembodiment, the processor 12 comprises at least one detection element 19for detecting the cassette 17 within the processor 12 and determining avariety of information about the cassette 17. The detection element 19transmits the information to the control element 15, and the controlelement 15 manipulates the processor 12 based on the information, aswill be discussed in more detail hereafter.

The reader 14 is configured to receive the cassette 17 after thecassette 17 has been processed by the processor 12 and to capture animage of a microarray (not shown) on the cassette 17. The microarrayindicates detection of the DNA, which is produced by PCR amplification.In one embodiment, the image of the microarray comprises a digitalimage, although other types of images are possible in other embodiments.The reader 14 is further configured to transmit the image to the controlelement 15 as test data in order to allow the control element 15 toanalyze the test data and compare the test data to the predefined data.

FIG. 2 depicts an exemplary embodiment of the control element 15 of FIG.1 . As set forth above, the control element 15 is coupled to at leastone processor 12 (FIG. 1 ) and at least one reader 14 (FIG. 1 ) of thesystem 10, and the control element 15 is configured to communicate with,monitor, and control the operation of the processor 12 and the reader14. The control element 15 is further configured to receive test datafrom the reader 14 and to analyze the test data, as will be discussed inmore detail hereafter. In one embodiment, the control element 15 isimplemented via a computer, such as a desktop or laptop computer, butother types of devices may be used to implement the control element 15in other embodiments.

As shown by FIG. 2 , the control element 15 comprises at least oneconventional processing element 20, such as a digital signal processor(DSP) or a central processing unit (CPU), that communicates to anddrives the other elements within the control element 15 via a localinterface 22, which can include at least one bus. The control element 15further comprises a processor interface 24 for enabling communicationwith the processor 12 and a reader interface 25 for enablingcommunication with the reader 14. In one embodiment, the processorinterface 24 receives status information from the processor 12 andallows the control element 15 to control the operation of the processor12 based on a plurality of settings, discussed in more detail hereafter.In one embodiment, the reader interface 25 receives status informationfrom the reader 14 and allows the control element 15 to control theoperation of the reader 14. Furthermore, the reader interface 25receives data from the reader 14 in the form of an image of themicroarray indicative of the amplified DNA from the specimen. Thecontrol element 15 further comprises a user input interface 26, such as,for example, a computer keyboard and/or mouse, and a user outputinterface 28, such as, for example, a computer monitor and/or printer.However, different user input and output interfaces 26 and 28 arepossible in other embodiments.

The control element 15 further comprises control logic 31 configured tocontrol the operation of the processor 12 and the reader 14 and tomanage data and other components within the control element 15. In thisregard, in one embodiment, the control logic 31 manages application ofan appropriate set of predefined settings 32 and an appropriate set ofpredefined data 35 for the cassette 17 by mapping the cassette 17 to theappropriate set of the settings 32 and the data 35 based on ID mappingdata 33 and/or information input by a user via the user input interface26. The ID mapping data 33 is stored in memory 30 of the control element15 and maps an identifier (not shown) on and associated with thecassette 17 (e.g., a bar code), as detected by the detection element 19(FIG. 1 ), to a corresponding set of predefined settings 32 and a set ofpredefined data 35 for that cassette 17. Each set of predefined settings32 is stored in memory 30 of the control element 15 and indicates avariety of operations to be executed by the processor 12 in order toperform arm-PCR for a corresponding cassette 17. Each set of predefineddata 35 indicates a set (e.g., one or more) of dots of the cassette'smicroarray that will fluoresce during reading due to DNA from a targetagent gathered at the dot, as will be discussed in more detailhereafter. The predefined data 35 is compared to test data 34 indicatingthe dots of the microarray that have fluoresced during reading in orderto determine whether the target agent is present in the specimen. Thepredefined settings 32 may vary depending on the type of tests being runon the specimen (e.g., the type of target agent the test is designed todetect in the specimen). For example, a set of the predefined settings32 may indicate information such as the length of time heaters (notshown in FIG. 2 ) are applied to the cassette 17 to perform arm-PCR fora target agent, the temperatures of the respective heaters, and theorder of specific operations to be performed by the processor 12 inorder to effectively manipulate the cassette 17 to perform arm-PCR forthe target agent, discussed in more detail hereafter.

In one embodiment, the predefined settings 32 include a plurality ofsets of operations to be performed by the processor 12. In one exemplaryembodiment, the predefined settings 32 include three sets of settings.In such embodiment, the three sets of settings 32 are tailored for highspecificity, high sensitivity, and nominal results. In this regard, ifthe set of the settings 32 tailored for high specificity is chosen, theprocessor 12 performs operations on the cassette 17 aimed at isolating aspecific target agent or DNA sequence in a specimen and excluding allother target agents or DNA sequences. However, if the set of settings,tailored for high sensitivity is chosen, the processor 12 performsoperations on the cassette 17 aimed at identifying a broad range oftarget agents or DNA sequences in a specimen. Furthermore, if thenominal set of settings is chosen, the processor 12 performs operationson the cassette 17 aimed at producing a nominal range of target agentsor DNA sequences. However, there may be a different numbers and types ofsets of settings in other embodiments.

In one embodiment, the sets of the predefined settings 32 may be usedfor a closed platform and an open platform. In this regard, the closedplatform allows specific tests to be performed for particular targetagents, such as, for example, Food and Drug Administration(FDA)-regulated target agents, while the open platform allows a widevariety of tests to be performed for unregulated target agents. Forexample, a set of the predefined settings 32 for the closed platform maybe automatically selected by the control logic 31 based on the targetagent as indicated by the ID mapping data 33. Thus, the user may notselect or otherwise control the test performed on the target agent onthe closed platform. However, for the open platform, the user maymanually select a desired set of the predefined settings 32 via the userinput interface 26 in order to obtain a desired result. In the exemplaryembodiment set forth above, the user may select one of three sets of thepredefined settings 32 to be performed on the cassette 17 wherein thesets are tailored for high specificity, high sensitivity, or nominalresults. However, different types and numbers of sets of the predefinedsettings 32 may be selected by the user on the open platform in otherembodiments. Furthermore, in one embodiment, the user may define acustom set of settings to be performed on the cassette 17 on the openplatform. Thus, on the open platform, the user may manipulate the testsperformed on the target agent by selecting different sets of thesettings 32 and varying primers that are used in the tests, as will bediscussed in more detail hereafter.

In an embodiment described above, an identifier for the cassette 17 isread by a detection element 19. In other embodiments, other techniquesfor determining the identifier are possible. As an example, theidentifier may be electronically stored in the cassette 17. The cassette17 may be configured to transmit the identifier wirelessly or otherwiseto the detection element 19. As an example, radio frequency (RF) orinfrared communication may be used to communicate the identifier. Inother embodiments, yet other techniques may be used by the detectionelement 19 to determine the cassette's identifier.

The control logic 31 is further configured to receive images of themicroarray from the reader 14 via the reader interface 25 and to storethe images in the memory 30 of the control element 15 as test data 34.In one embodiment, the test data 34 comprises one or more digital imagesof the microarray for one or more cassettes 17, although different typesof test data 34 are possible in other embodiments. The control logic 31is further configured to compare the test data 34 to the predefined data35 mapped to the cassette 17 in order to determine whether particulartarget agents are detected in the specimen. In this regard, in oneembodiment, the test data 34 comprises an image of the microarraywherein DNA corresponding to a particular target agent is gathered at aspecific dot or combination of dots (not shown) in the microarray. Thedot or combination of dots at which the DNA is gathered fluoresce whenilluminated with laser light from the reader 14. The reader 14 capturesa digital image of the microarray while the microarray is illuminated bya laser, and microarray detection logic 36 is configured to analyze theimage to determine which dots fluoresce due to the presence of DNA on orin the dot. As described in more detail herein, each dot is composed ofa different material, and the dots are arranged in a predefined pattern.Thus, the pattern of fluorescing dots in the image indicates whether thetarget agent is present in the sample under test. Moreover, the logic 36digitally analyzes the image to determine which dots are fluorescing inthe image and compares the determined fluorescing pattern to theappropriate set of predefined data 35 for a particular target agent.Based on such comparison, the logic 36 determines whether the targetagent is present in the sample under test.

In analyzing the microarray image the logic 36 locates and identifieseach dot within the image. There are various techniques that can be usedto locate and identify dots. In one exemplary embodiment, the logic 36identifies area within the digital image, referred to herein as “testareas.” Each test area is an area of the digital image in which aparticular dot is expected to be located based on the predefined patternof dots on the microarray. As an example, FIG. 23 depicts a portion of amicroarray image showing an exemplary dot 101. The reference line 102,which is not actually visible in the image, represents a test area 103in which the logic 36 expects to find a dot 101 based on the pixellocations of the test area 103 within the digital image. To determinewhether the dot 101 associated with the test area 103 is fluorescing inthe image, the logic 36 averages the brightness of all of the pixelswithin the test area 103 and compares the averaged brightness to athreshold. If the average brightness exceeds the threshold, then thelogic 36 determines that the dot 101 is fluorescing in the image.However, if the average brightness does not exceed the threshold, thenthe logic 36 determines that the dot 101 is not fluorescing in theimage.

As shown by FIG. 23 , the dot 101 may be slightly misaligned with thetest area 103 for a variety of reasons, including imperfections indepositing the material of the dot 101 on the microarray. Suchmisalignment could result in a false fluorescent determination if asignificant portion of the test area 103 is not aligned with the dot101. Thus, in an effort to improve the test results, the logic 36automatically moves the image of the dot 101 relative to the test area103 so that a greater percentage of the dot 101 is within the test area103. In this regard, before assessing whether the associated dot 101 isfluorescing, as described above, the logic 36 performs an alignmentalgorithm to reposition the dot 101 within the microarray image.

According to such algorithm, the logic 36 identifies the dot 101 bycomparing the pixel color values. In this regard, a group of contiguouspixels having substantially similar color values generally indicate thelocation of the dot 101 within the image.

After identifying the dot 101, the logic 36 is configured to measure theaverage brightness of the test area 103 associated with the dot 101(e.g., closest to the dot 101 within the image). The logic 36 thenslightly repositions the dot 101 relative to the test area 103 (e.g.,moves the dot 101 within the image), as shown by FIG. 24 , and againaverages the brightness of the pixels within the test area. If themovement causes a greater percentage of the test area 101 to be coveredby the dot 101, then the average brightness should increase after themovement. The logic 26 compares the average brightness prior to themovement to the average brightness after the movement, and determineswhether the dot 101 is more aligned based on such comparison. In thisregard, if the average brightness after the repositioning is higher,then the logic 36 determines that the dot 101 is now more aligned withthe test area 101. However, if the average brightness is afterrepositioning is less, then the logic 36 determines that the dot 101 isnow less aligned with the test area 101.

Moreover, the logic 36 continues repositioning the dot 101 and measuringaverage brightness until a maximum average brightness is found. Theposition of the dot 101 relative to the test area 103 for such maximumbrightness is the position that results in the greatest degree ofalignment between the dot 101 and the test area 103. Such position isselected by the logic 103 as the final position within the image to beused for the dot 101.

In one exemplary embodiment, the logic 36 moves the dot 101 in awidening spiral relative to the test area 103 when performing therepositioning algorithm. In this regard, the logic 36 moves the dot 101such that its center moves along a spiral 104, as shown by FIG. 23 . Aslong as the average brightness of the test area 103 continues toincrease for successive number of positions of the dot 101, the logic 36continues repositioning the dot 101. However, once the averagebrightness decreases for a successive number of dot positions, the logic36 stops the repositioning algorithm and selects the position thatprovided the highest average brightness as the dot's final positionwithin the image. In other embodiments, other techniques and/or movementpatterns may be used to find the position for which the dot 101 is mostaligned with the test area 103. In one exemplary embodiment, the logic36 is configured to perform the same repositioning algorithm separatelyfor each dot of the microarray image such that each dot is individuallymoved to better align it with its respective test area. Once all of therespective dots have been repositioned, the image is stored in memory 30as test data 34.

The predefined data 35 is stored in memory 30 and indicates for a givencassette 17 one or more dots in the microarray corresponding to aparticular target agent. In this regard, the predefined data 35indicates one or more dots in the microarray that should fluoresceduring reading when DNA from a particular target agent is present in thespecimen. Thus, if the test data 34 indicates that DNA is detected atone or more particular dots in the microarray, the control logic 31accesses the predefined data 35 mapped to the cassette 17 to determinewhich target agent corresponds with the dots. The control logic 31performs the comparison for each dot in the microarray in order to testfor one or more target agents. The control logic 31 transmits results ofthe comparison between the test data 34 and the predefined data 35 viathe user output interface 28. In one embodiment, the control logic 31stores the test results in the memory 30 as test results data 37 whichthe user may access via the user output interface 28. For example, forthe closed platform, the test results data 37 may indicate a “yes” or“no” for each target agent for which the test is being run in order toindicate whether such target agent is detected in the specimen, butdifferent types of indications are possible. However, for the openplatform, the test results data 37 may indicate a value for each dotindicative of the brightness of the dot such that the user may comparevarious sets of the test results data 37 for a given target agent inorder to determine a preferred solution for the target agent, discussedin more detail hereafter.

It should be noted that the control logic 31 and the microarraydetection logic 36 can be implemented in software, hardware, firmware orany combination thereof. In an exemplary embodiment illustrated in FIG.2 , the control logic 31 and the microarray detection logic 36 areimplemented in software and stored in memory 30 of the control element15.

Note that the control logic 31 and the microarray detection logic 36,when implemented in software, can be stored and transported on anycomputer-readable medium for use by or in connection with an instructionexecution apparatus that can fetch and execute instructions. In thecontext of this document, a “computer-readable medium” can be any meansthat can contain or store a computer program for use by or in connectionwith an instruction execution apparatus.

FIG. 3 depicts an exemplary processor module 40 of the processor 12 ofFIG. 1 . In this regard, the processor 12 comprises one or moreprocessor modules 40. In one embodiment, the processor 12 comprises fourprocessor modules 40 positioned side by side within a housing (notshown), although any number of modules 40 may be utilized in otherembodiments. Each processor module 40 is configured to receive andprocess a single cassette 17 (FIG. 1 ) such that arm-PCR techniques areperformed upon a specimen within the cassette 17. The processor module40 comprises a receptacle 42 for receiving and housing the cassette 17while the cassette 17 is located within the module 40. The module 40further comprises at least one detection element 19 located adjacent tothe receptacle 42 for detecting an identifier (not shown) located on anouter surface of the cassette 17 when the cassette 17 is positionedwithin the receptacle 42. In one embodiment, the detection element 19comprises a barcode scanner and the identifier comprises a barcode,although other types of detection elements 19 and identifiers may beused in other embodiments. The detection element 19 detects theidentifier and transmits the identifier to the control element 15 (FIG.1 ) in order to allow the control element 15 to map the identifier tothe predefined settings 32 (FIG. 2 ), as set forth above.

Once the predefined settings 32 are determined, the control element 15communicates with an onboard control element 48 which controls theoperation of the processor module 40 based upon the settings 32. In thisregard, the onboard control element 48 controls the operation of a latchmotor 41, a cam bar motor 43, a pump pin motor 44, a lead screw motor45, a heater assembly 46, and a lifter assembly 47. The latch motor 41controls the operation of a latch (not shown), discussed in more detailhereafter. The cam bar motor 43 is coupled to a cam bar shaft 50 andcontrols rotation of the cam bar shaft 50, as will be discussed in moredetail hereafter. In one embodiment, the cam bar motor 43 is positionedbehind the receptacle 42 within the module 40. The cam bar shaft 50extends horizontally into a rear opening (not shown) of the receptacle42 and engages with a cam bar (not shown) of the cassette 17 in order tocontrol clockwise and counterclockwise rotation of the cam bar andmanipulate movement of a pipette (not shown) upward and/or downward in avertical direction within the cassette 17. The pump pin motor 44 iscoupled to a plunger 52 and controls lateral movement of the plunger 52,discussed in more detail hereafter. The pump pin motor 44 is positionedbehind the receptacle 42 within the module 40, and the plunger 52extends laterally into the receptacle 42 via an opening (not shown) inthe receptacle. The plunger 52 engages with a pump pin (or “push rod”)(not shown) of the cassette 17 and operates a pipette pump assembly (notshown) within the cassette 17 such that fluid is either drawn into thepipette or expelled from the pipette due to the plunger 52 compressingthe pump pin.

Furthermore, the lead screw motor 45 is rotatably coupled to a leadscrew shaft 53 and controls clockwise and counterclockwise rotation ofthe lead screw shaft 53. In one embodiment, the lead screw motor 45 ispositioned behind the receptacle 42 within the module 40, and the leadscrew shaft 53 extends horizontally into the receptacle 42. The leadscrew shaft 53 engages with the lead screw (not shown) of the cassette17 in order to control lateral movement of the pipette within thecassette 17. In this regard, rotating the lead screw shaft 53 in aclockwise direction causes the lead screw to rotate in a clockwisedirection such that the pipette travels laterally in one directionwithin the cassette 17, while rotating the lead screw shaft 53 in acounterclockwise direction causes the lead screw to rotate in acounterclockwise direction such that the pipette travels laterally inthe opposite direction within the cassette 17. Control of the cam bar,pump pin, and lead screw of the cassette 17 allows the module 40 tomanipulate the pipette within the cassette 17 such that the pipetteremoves fluids from reagent chambers (not shown) or a sample chamber(not shown) within the cassette 17, or injects fluids into a reagentchamber or detection chamber (not shown) within the cassette 17.

The heater assembly 46 comprises a plurality of heaters 55. In oneembodiment, the heater assembly 46 comprises three heaters 55, althoughother numbers of heaters 55 are possible in other embodiments. In oneembodiment, the heater assembly 46 is positioned directly below thereceptacle 42 within the module 40. Each heater 55 is positioned upon anadjustable base 56 which may move in a vertical direction to adjust thevertical position of the heater 55, as will be described in more detailhereafter. In one embodiment, each heater 55 is set at a particulartemperature and remains at that temperature while the module 40 is inoperation. For example, in one embodiment, one heater 55 is set at 55degrees Celsius, one heater 55 is set at 72 degrees Celsius, and oneheater 55 is set at 95 degrees Celsius, although different temperaturesare possible in other embodiments. However, the temperature of eachheater 55 may vary at different times during operation in otherembodiments. Each heater 55 has a recess (not shown in FIG. 3 ) forreceiving the sample chamber located in a bottom of the cassette 17. Thespecimen is inserted into the sample chamber, and the heaters 55 engagewith the sample chamber at various times in order to heat the chamberduring the performance of arm-PCR on the specimen. Furthermore, in oneembodiment, one heater 55 may be raised to contact a microarray (notshown) in a bottom of the detection chamber in order to performhybridization and extraction.

The heater assembly 46 further comprises a base motor 57, a base plate58 and a track 59. The base plate 58 is coupled to each of theadjustable bases 56, and the base plate 58 slideably engages with thetrack 59 in order to facilitate horizontal movement of the heaters 55along the track 59. In one embodiment, the motor 57 rotatably engageswith the base plate 58 in order to facilitate horizontal movement(parallel to the x-direction) of the base plate 58. Thus, whenadjustment of the horizontal position of the heaters 55 is desired, themotor 57 causes the base plate 58 to slide horizontally along the track59 a desired distance.

The module 40 further comprises the lifter assembly 47 positionedbeneath the heater assembly 46. The lifter assembly 47 comprises atleast one cam 60 and at least one sensor 61. In one embodiment, theassembly 47 comprises two cams 60 and two sensors 61, although othernumbers of cams 60 and sensors 61 are possible in other embodiments.Also, the cams 60 are configured to rotate and contact a heater base 56in order lift the heater 55 into contact with the sample chamber ordetection chamber of the cassette 17. In one embodiment, each cam 60 issnail-shaped such that the cam 60 does not contact any of the heaterbases 56 when the cam 60 is in a home position, but the cam 60 contactsand lifts the heater base 56 when the cam 60 is in an engaged position.However, different cam shapes are possible in other embodiments.Furthermore, in one embodiment, one cam 60 is configured to lift theheaters 55 to the sample chamber and one cam 60 is configured to liftone heater to the microarray on the detection chamber. However, otherconfigurations are possible in other embodiments. The sensor 61corresponding to each cam 60 is configured to detect whether the cam 60is in the home position and to transmit such detection to the onboardcontrol element 48 of item 40.

FIG. 4 depicts a rear perspective view of the processor module 40 ofFIG. 3 . As shown in FIG. 4 , in one embodiment, the cam bar motor 43 iscoupled to a pulley 65 via a belt 66. The pulley 65 is positioned aroundand coupled to an outer surface of the cam bar shaft 50. The cam barmotor 43 is coupled to the onboard control element 48, which controlsthe operation of the motor 43 based on the predefined settings 32, asset forth above. When the motor 43 rotates, the belt 66 rotates in themotor's direction of rotation thereby engaging the pulley 65 and causingthe cam bar shaft 50 to rotate in the same direction. As set forthabove, rotation of the cam bar shaft 50 causes rotation of thecassette's cam bar which adjusts the vertical position of the pipettewithin the cassette 17. In one embodiment, a cam bar shaft sensor 67 ispositioned behind the cam bar shaft 50 and the pulley 65, and the cambar shaft sensor 67 detects the cam bar shaft 50 when the shaft 50extends through the sensor 67. The sensor 67 transmits a signal to thecontrol element 48 (FIG. 3 ) when the cam bar shaft 50 is detected inorder to detect insertion of the cassette 17 and maintain the cassette17 within the receptacle 42 for processing.

The pump pin motor 44 is coupled to the plunger 52 (FIG. 3 ) andcontrols the horizontal position of the plunger 52. In one embodiment,the pump pin motor 44 comprises a linear motor, although other types ofmotors 44 are possible in other embodiments. The motor 44 is coupled tothe onboard control element 48, and the control element 48 controls theoperation of the motor 44 in order to manipulate the plunger 52 forperforming arm-PCR within the cassette 17, as set forth above.

The lead screw motor 45 is coupled to a pulley (not shown in FIG. 4 )which is coupled around an outer surface of the lead screw shaft 53. Inone embodiment, the lead screw motor 45 is coupled to the pulley via abelt 68. When the motor 45 rotates, the belt 68 rotates in the samedirection and engages the pulley such that the pulley and the lead screwshaft 53 pivot in the same direction. Rotation of the lead screw shaft53 causes the lead screw of the cassette 17 to rotate thereby adjustingthe horizontal position of the pipette within the cassette 17 andfacilitating arm-PCR. The module 40 further comprises a lead screw shaftsensor 69 positioned behind the lead screw shaft 53 and the pulley. Thesensor 69 is configured to detect the shaft 53 and inform the controlelement 48 of the shaft's position in order to ensure that the shaft 53has properly engaged with the cassette 17.

FIG. 5 depicts the heater assembly 46 of FIG. 3 . The heater assembly 46comprises the heaters 55, the bases 56, the base motor 57, the baseplate 58, and the track 59. In one embodiment, the heater assembly 46comprises three heaters 55 and three bases 56, although other numbers ofheaters 55 and bases 56 are possible in other embodiments. Each heater55 is positioned upon a base 56, and each base 56 is slideably coupledto the base plate 58. In this regard, each base 56 is coupled to thebase plate 58 such that the base 56 may freely move upward and downward(parallel to the y-direction). The cam 60 (FIG. 3 ), discussed in moredetail hereafter, contacts the base 56 and causes the base 56 to slidevertically (parallel to the y-direction) with respect to the base plate58 in order to bring the heater 55 into contact with the sample chamberor the detection chamber of the cassette 17. Furthermore, each heater 55has a recess 70 located in a top surface of the heater 55 for receivingthe sample chamber of the cassette 17, as will be discussed in moredetail hereafter.

The base plate 58 is slideably coupled to the track 59 such that thehorizontal position of the base plate 58 may be adjusted. The motor 57controls the movement of the base plate 58. Thus, when a desired heater55 is required by the settings 32 to come into contact with the cassette17, the motor 57 adjusts the horizontal position of the base plate 57such that the desired heater 55, when raised vertically, will come intocontact with the cassette 17. In one embodiment, the base plate 58engages with the track 59 and has a threaded channel (not shown) forreceiving a horizontally-oriented threaded rod 71. The rod 71 is coupledto the motor 57, and rotation of the motor 57 causes rotation of the rod71 thereby adjusting the horizontal position of the base plate 58 alongthe track 59. However, other means for adjusting the position of theheaters 55 are possible in other embodiments.

FIG. 6 depicts an exemplary embodiment of the heater 55 of FIG. 3 . Inone embodiment, the heater 55 comprises metal, although other materialsare possible in other embodiments. The heater 55 has a flat top surface73 having a concave recess 70 extending down into the surface 73. Therecess 70 is dimensioned to receive the sample chamber of the cassette17 (FIG. 1 ) such that the chamber fits in the recess 70 and an exteriorsurface of the chamber contacts the surface defining the recess 70.

In one embodiment, the heater 55 comprises at least one magnet (notshown) positioned in close proximity to the recess 70. In oneembodiment, the heater 55 comprises a plurality of electromagnets thatmay be selectively activated in order to magnetically couple to metallicbeads (not shown) within the sample chamber when desired. In thisregard, the onboard control element 48 sends a control signal to theheater 55 in order to activate an electromagnet in the heater therebycreating a magnetic flux, which magnetically couples to the beads withinthe chamber. The beads bond to DNA from the specimen, and theelectromagnet magnetically couples to the beads through the samplechamber in order to position the beads in a desirable orientation withinthe chamber. Magnetically coupling with the beads facilitates steps inthe arm-PCR process, such as, for example, addition and/or removal offluids, without inadvertent removal of the beads from the chamber. As anexample, the electromagnets may magnetically couple with the beads inorder to hold the beads in the bottom of the sample chamber. The magnetsalso provide adequate spacing of the beads within the chamber such thatall of the DNA attached to the beads is exposed to the arm-PCR process.Other types of magnets, such as, for example, permanent magnets, arepossible in other embodiments. When the heater 50 is lifted to theengaged position and receives the sample chamber, the heater 55transfers heat to the chamber thereby performing steps in the arm-PCRprocess.

In one exemplary embodiment, an electromagnet close to the bottom of therecess 70 is activated to pull the beads toward the bottom of the samplechamber. To stir or mix the beads, such electromagnet is deactivated,and another electromagnet magnet (e.g., one close to a side of therecess 70) is activated to move the beads from the chamber bottom. Theactivation states of the electromagnets are then reversed to pull thebeads to the bottom of the sample chamber again. However, in otherembodiments, the magnets may comprise permanent magnets that areactivated and deactivated by raising and lowering the magnets,respectively.

The heater 55 further comprises an electrical interface 75 located on aside of the heater 55. The interface 75 receives power from a powersupply (not shown) thereby enabling the heater 55 to reach a desiredtemperature as set forth in the predefined settings 32 (FIG. 2 ). Inthis regard, the heater 55 has internal or external resistive elements(not shown) that generate heat when electrical current is appliedthereto. Thus, the control element 48 can control when heat is generatedby the heater 55 by controlling an electrical signal that is applied tothe resistive elements through the electrical interface 75. Theinterface 75 also communicates with the control element 48, and thecontrol element 48 communicates with the control element 15 via theprocessor interface (FIG. 2 ) and allows the control logic 31 toactivate the desired magnets within the heater 55 based on the settings32.

FIG. 7 depicts an exemplary embodiment of the lifter assembly 47 of FIG.3 . As set forth above, in one embodiment, the lifter assembly 47comprises at least one cam 60 and at least one sensor 61. The assembly47 further comprises a base unit 77, the cams 60 and the sensors 61. Thearms 60 are rotatably coupled to the base unit 77. In one embodiment,the base unit 77 contains at least one motor (not shown) for controllingrotation of the cams 60, and the base unit 77 is coupled to the onboardcontrol element 48. The onboard control element 48 communicates with thecontrol element 15 (FIG. 1 ) in order to allow the control logic 31(FIG. 2 ) to control the rotation of the cams 60 based upon thepredefined settings 32 (FIG. 2 ).

The sensors 61 are also coupled to the onboard control element 48, andthe sensors 61 are configured to detect whether the corresponding cams60 are in the home position and to transmit such detection to thecontrol element 48. In one embodiment, the sensors 61 comprise proximitysensors, although other types of sensors 61 are possible in otherembodiments. The control element 48 controls rotation of the cams 60based upon a comparison of the detections to the desired orientation ofthe cams 60 as defined in the applicable settings 32. For example, ifthe sensor 61 detects that the cam 60 is in the home position but theheater 55 positioned above the cam 60 is required by the settings 32 tobe heating the cassette 17, the control element 48 causes the motor torotate thereby rotating the cam 60 to the engaged position, which causesthe cam 60 to contact the base 56 and lift the heater 55 to the engagedposition.

In one embodiment, one cam 60 is positioned beneath the cassette 17 whenthe cassette 17 is within the receptacle 42 (FIG. 3 ) such that the cam60 is vertically-aligned with the sample chamber. Thus, when the cam 60is rotated to the engaged position, the heater 55 aligned above the cam60 will be lifted to the sample chamber such that the recess 70 (FIG. 6) will receive the sample chamber. Furthermore, in one embodiment, theother cam 60 is positioned beneath the cassette 17 such that the cam 60is vertically-aligned with the detection chamber and the heater 55aligned above the cam 60 will contact the microarray when the cam 60 isrotated to the engaged position. However, other orientations of the cams60 are possible in other embodiments.

FIG. 8 depicts an exemplary embodiment of the cam bar shaft 50 of FIG. 3. In one embodiment, the cam bar shaft 50 comprises metal, althoughother materials are possible. The cam bar shaft 50 comprises a shaftportion 80 having a slot 81. The shaft portion 80 extends from thepulley 65 (FIG. 4 ) and into the receptacle 42 (FIG. 3 ). The slot 81receives a knob (not shown) located on an end of the cam bar of thecassette 17 (FIG. 1 ). Thus, rotation of the cam bar motor 43 causesrotation of the shaft portion 80 thereby causing rotation of the cam bardue to the engagement of the slot 81 with the cam bar. Rotation of thecam bar adjusts the vertical position of the pipette within the cassette17, as set forth above. While the cam bar shaft 50 of FIG. 8 has a slot81, other means for engaging with the cam bar are possible in otherembodiments.

9 depicts an exemplary embodiment of the plunger 52 of FIG. 3 . In oneembodiment, the plunger 52 comprises metal, although other types ofmaterials are possible. The plunger 52 comprises a base portion 85 and atip 86. The base portion 85 extends from the pump pin motor 44 (FIG. 3), and the tip 86 extends from the base portion 85 to the pump pin ofthe cassette 17. The pump pin motor 44 causes the plunger 52 to move ina horizontal direction thereby causing the pipette to release and expelfluids within the cassette 17, as set forth above. While the plunger 52is disclosed in FIG. 9 , other means for engaging the pump pin arepossible in other embodiments.

10 depicts an exemplary embodiment of the lead screw shaft 53 of FIG. 3. In one embodiment, the lead screw shaft 53 comprises metal, althoughother materials are possible. The lead screw shaft 53 comprises a shaftportion 88 having a slot 89. The shaft portion 88 extends from thepulley (not shown in FIG. 4 ) coupled to the lead screw motor 45 (FIG. 3) and into the receptacle 42 (FIG. 3 ). The slot 89 receives a knob (notshown) located on an end of the lead screw of the cassette 17 (FIG. 1 ).Thus, rotation of the lead screw motor 45 causes rotation of the shaftportion 88 thereby causing rotation of the lead screw due to theengagement of the slot 89 with the lead screw. Rotation of the leadscrew adjusts the horizontal position of the pipette within the cassette17, as set forth above. While the lead screw shaft 53 of FIG. 10 has aslot 89, other means for engaging with the lead screw are possible inother embodiments.

FIG. 11 depicts a heater 55 receiving the sample chamber of the cassette17. The cassette 17 is positioned within the receptacle 42. As shown byFIG. 11 , the lifter assembly 47 engages with the heater assembly 46. Inthis regard, the cam 60 of the lifter assembly 47 is rotated to theengaged position such that the cam 60 is contacting the base 56 of aheater 55. The contact between the cam 60 and the base 56 causes thebase 56 to elevate with respect to the base plate 58 such that theheater 55 is lifted upward toward the receptacle 42.

The recess 70 (FIG. 6 ) of the heater 55 receives the sample chamber(not shown) which extends from a bottom surface of the cassette 17. Theheater 55 transfers heat and/or a magnetic field to the sample chamberin order to perform steps in the arm-PCR process. The cam 60 remains inthe engaged position such that the heater 55 contacts the cassette 17until the control logic 32 (FIG. 2 ) instructs the cam 60 to return tothe home position based upon the predefined settings 32. When the cam 60returns to the home position, the cam 60 rotates out of contact with thebase 56 such that the base 56 returns to a lowered position with respectto the base plate 58 due to gravity or a return spring (not shown).

FIG. 12 depicts an exemplary embodiment of the reader 14 of FIG. 1 . Inone embodiment, the reader 14 comprises a drive assembly 95, a flywheelassembly 96, and an optics assembly 97 positioned within a housing 98.The drive assembly 95 is positioned above the flywheel assembly 96, andthe drive assembly 95 is configured to engage with the flywheel assembly96 and control rotation of the flywheel assembly 96, as will bediscussed in more detail hereafter. The drive assembly 95 comprises alarge sheave 100, a small sheave 101, and a belt 102. The belt 102 fitstightly around the large sheave 100 and the small sheave 101 such thatrotation of the small sheave 101 causes rotation of the large sheave 100due to the belt 102. The small sheave 101 is coupled to a motor (notshown) via a polyflex shaft (not shown in FIG. 12 ) extending downwardlyfrom the drive assembly 95, and the motor controls rotation of the smallsheave 102. The large sheave 102 is coupled to the flywheel assembly 96via a flywheel shaft (not shown in FIG. 12 ). Therefore, the motorcontrols rotation of the flywheel assembly 96 via the drive assembly 95.

The flywheel assembly 96 comprises a flywheel 105 and a plurality ofreceptacles 106 positioned upon a top surface of the flywheel 105. Inone embodiment, the flywheel 105 is circular and has four receptacles106 positioned upon the flywheel 105, but other numbers of receptaclesand shapes of the flywheel 105 are possible in other embodiments. Eachreceptacle 106 is dimensioned to receive a cassette 17 (FIG. 1 ).Furthermore, each receptacle 106 faces an edge of the flywheel 105 suchthat the cassette 17 may be inserted into each receptacle 106 when suchreceptacle is oriented toward a front of the reader 14. The flywheel 105has a plurality of openings (not shown in FIG. 12 ) for allowing theoptics assembly 97 to detect a microarray of each cassette 17 positionedwithin the flywheel assembly 96, as will be discussed in more detailhereafter. The flywheel assembly 96 is configured to rotate at a highspeed in order to allow the optics assembly 97 to quickly scan themicroarray of each cassette 17 within the assembly 96.

The optics assembly 97 is slideably mounted to a flywheel support plate110 of the housing 98. The optics assembly 97 is configured to detectthe microarray of each cassette 17 positioned within the flywheelassembly 96 and to transmit data indicative of the microarray to a localcontrol element 109. The control element 109 communicates with thecontrol element 15 (FIG. 1 ) in order to control the operation of thecomponents of the reader 14. The optics assembly 97 slides slowly alonga track 108 positioned on the support plate 110 of the housing 98 suchthat the assembly 97 scans the entire microarray of each cassette 17within the rotating flywheel assembly 96, as will be discussed in moredetail hereafter.

FIG. 13 depicts the reader 14 of FIG. 12 with the drive assembly 95removed. As shown in FIG. 13 , the flywheel assembly 96 comprises theflywheel 105 and a plurality of receptacles 106 positioned upon theflywheel 105. Each receptacle 106 receives a cassette 17. The flywheel105 is positioned upon the flywheel support plate 110 rigidly mounted tothe housing 98. The flywheel 105 is rotatably mounted to the supportplate 110 and rotates 360 degrees with respect to the support plate 110.The support plate 110 has an opening (not shown) for allowing light fromthe optics assembly 97 to pass through to the microarray of the cassette17 in order to allow the optics assembly 97 to capture data indicativeof target agents detected by the microarray.

FIG. 14 depicts the reader 14 of FIG. 12 with the drive assembly 95 andthe flywheel assembly 96 removed. The optics assembly 97 comprises anoptical cube assembly (OCA) 114 and a laser 115 (not shown in FIG. 14 ),discussed in more detail hereafter, mounted to a mounting plate 116. TheOCA 114 comprises a lens 117 for detecting a microarray of each cassette17 (FIG. 1 ) positioned within the flywheel assembly 96 (FIG. 12 ). Theoptics assembly 97 is coupled to the control element 109, and the opticsassembly 97 is configured to transmit a signal indicative of an image ofthe microarray for each cassette 17 to the control element 15. Thecontrol element 15 compares the image of each cassette 17 to thepredefined data 35 for the cassette 17 in order to determine whether atarget agent has been detected in a specimen within the cassette 17.

The reader 14 further comprises a power supply 120 configured to supplypower to components of the reader 14. The power supply 120 may supplyelectrical power for powering electrical components of the reader 14,such as the laser 115, the motors (not shown), and the sensors (notshown in FIG. 14 ).

FIG. 15 depicts an exemplary embodiment of the drive assembly 95 of thereader 14 of FIG. 12 . As set forth above, the drive assembly 95comprises a large sheave 100, a small sheave 101, and a belt 102. Thelarge sheave 100 is generally circular, and the large sheave 100 isvertically aligned with the flywheel 105 (FIG. 12 ). The large sheave100 is coupled to a flywheel shaft (not shown), and the flywheel shaftextends downward from a center of the large sheave 100 to a center ofthe flywheel 105 in order to couple the large sheave 100 to the flywheel105.

The small sheave 101 is vertically-aligned with a motor (not shown). Thesmall sheave 101 is coupled to a polyflex shaft 123, and the shaft 123extends downwardly from the small sheave 101 to the motor in order tocouple the small sheave 101 to the motor. The small sheave 101 iscoupled to the shaft 123 via a coupling mechanism 125. In oneembodiment, the coupling mechanism 125 comprises a dowel pin, a screw, anut, and a washer wherein the screw engages with a threaded channelwithin the shaft in order to couple the small sheave 101 to the shaft123. However, other types of coupling mechanisms 125 are possible inother embodiments. The motor controls rotation of the polyflex shaft123, and rotation the polyflex shaft 123 causes rotation of the smallsheave 101. The belt 102 is positioned around the large sheave 100 andthe small sheave 101 such that the belt is stretched tightly androtation of one sheave 100 and 101 results in rotation of the othersheave 100 and 101. Accordingly, rotation of the motor causes rotationof the small sheave 101, and rotation of the small sheath 101 causesrotation of the large sheave 100 via the belt 102. Rotation of the largesheave 100 causes rotation of the flywheel 105. Therefore, the motorcontrols rotation of the flywheel 105 via the drive assembly 95.

FIG. 16 depicts an exemplary embodiment of the flywheel assembly 96 ofFIG. 12 . As set forth above, the flywheel assembly 96 comprises theflywheel 105 and a plurality of receptacles 106 positioned on a topsurface of the flywheel 105. Each receptacle 106 is dimensioned toreceive a cassette 17 (FIG. 1 ). In one embodiment, the flywheelassembly 96 comprises four receptacles 106 positioned perpendicularly toone another. Accordingly, the reader 14 may read four cassettes 17simultaneously. Furthermore, in one embodiment, a plurality of readers14 may be coupled to one another in order to read a plurality ofcassettes 17 simultaneously. For example, twelve readers 14 may beconnected in order to process forty-eight cassettes 17 simultaneously.However, other numbers of cassettes 17 may be read simultaneously by thereader 14 in other embodiments. In one embodiment, each receptacle 106comprises an auto-balancer (not shown) for maintaining the flywheel'sbalance during the reading process when a cassette 17 is not positionedwithin each receptacle.

A flywheel shaft (not shown) extends vertically from a center of theflywheel 105 between the backs of the receptacles 106 in order to couplethe flywheel 105 to the large sheath 100, as set forth above. Theflywheel 105 freely rotates 360 degrees with respect to the flywheelsupport plate 110 (FIG. 13 ) in order to allow each cassette 17 to beoriented toward a front of the reader 14 (FIG. 12 ) as desired. Notethat each receptacle 106 is positioned such that the microarray of thecassette 17 is aligned with an opening (not shown in FIG. 16 ) in theflywheel 105 in order to allow the optics assembly 97 to detect themicroarray when the cassette 17 is positioned within the receptacle 106.

The flywheel 105 rotates at a high rate of speed, for instance at levelsabove 400 rpm. The flywheel 105 and other associated parts are subjectto increased levels of kinetic energy during high speed rotation. As aresult, the load in the flywheel 105 must be carefully balanced. Smalldifferences in mass load can result in a large force imbalance when theflywheel 105 is rotating at high speed. Unbalanced flywheels 105 maypermanently damage the reader 14 or other device components, causeinjury to users of the device or cause contamination of the sample.Generally, balancing the flywheel 105 is achieved by using a combinationof cassettes 17 and balance devices which all have the same weight or byusing various balancing patterns without balance devices.

FIGS. 25 and 26 depict an exemplary embodiment of the flywheelreceptacle 106. In one embodiment, the receptacle 106 comprises ahousing 200. Turning now to FIG. 25 , the housing 200 comprises a firstside 202 with an angled recess 204. The recess 204 has evenly spaced anddimensionally identical teeth 206 on the upper 208 and lower 210 sides.The teeth 206 project inwardly into the angled recess 204.

FIG. 26 illustrates a second side 212 of housing 200. The second side212 has an angled recess 214 with evenly spaced and dimensionallyidentical teeth 216 on the lower side 218 (not shown, see FIG. 16 ). Theteeth 218 project into the angled recess (FIG. 16 ). The first side 202and second side 212 contain locking tabs 220 with both male pins 222 andfemale slots 224. Connecting the locking tabs 220 securely links thefirst side 202 and second side 212. When joined, the first side 202 andsecond side 212 form the receptacle 106 which receives the cassette 17.

FIG. 27A depicts a geared weight 240 for use in balancing a flywheel 105containing an uneven number of cassettes 17 during high speed rotation.The geared weight 240 comprises a first side 242 with two rotatingpinion gears 246, 250. Gears 246, 250 each comprise a disk with radiallyprojecting interlocking teeth 248, 252. The edge of each tooth 248, 252is straight and aligned parallel to the axis of rotation. Gears 246 and250 are precisely sized to allow their mounting into the angled recess204 on the first side 202 of the housing 200 (FIG. 25 ). Here, the gearteeth 248, 252 engage with non-rotating teeth 206 (FIG. 16 ). Referringto FIGS. 27A and 27C, weight 240 also comprises a second side 244 withone rotating pinion gear 254 with teeth 256. Gear 254 is precisely sizedto fit into angled recess 214 on the second side 212 of housing 202.Teeth 256 engage with the non-rotating teeth 216 (FIG. 16 ). The precisealignment of gears 246, 250 and 254 with non-rotating teeth 206 allowsmovement of the weight 240 up and down the angled recesses 204 and 214.Engagement of gear teeth 248, 252 and 256 with the non-rotating teeth206 maintains weight 240 in an upright position and prevents the weight240 from tipping, spinning or otherwise becoming misaligned withinangled recesses 204 and 214.

FIG. 13 depicts an exemplary embodiment of the flywheel receptacle 106containing a cassette 17. In this embodiment, a cassette 17 is insertedinto the receptacle 106. Intersection of the cassette 27 into thereceptacle 106 brings the back end 265 of cassette 17 into contact withthe weight 240. Movement of the cassette 17 into the receptacle exerts aforce onto weight 240 and initiates rotation of gears 246, 250 and 254.This rotation causes the engagement and disengagement of gear teeth 248252 and 256 with non-rotating teeth 206, resulting in the movement ofweight 240 up the angled recesses 204, 214. Complete insertion of the 17cassette deposits weight 240 at the end of receptacle 106 opposite ofwhere the cassette was inserted. Weight 240 is now located near thecenter of flywheel 106 and is prevented from moving down the receptacleby the presence of cassette 17 (FIG. 13 ). The weight 240 will thereforemaintain this central location even during rotation of the flywheel 106at high speeds. In addition, the center of balance of flywheel 106 willremain at or near the midpoint of the device, preventing any forceimbalance during rotation.

In an additional embodiment, the cassette 17 is removed from receptacle106. Gravitational forces cause the weight 240 to move down the angledrecesses 204, 214. These forces cause rotation of gears 246, 250 and 254and the engagement and disengagement of gear teeth 248 252 and 256 withnon-rotating teeth 206. Weight 240 moves down angled recesses 204, 214until gears 246, 250 and 254 rest against the bottom edge 260 of angledrecesses 204 and 214. Bottom edge 260 then prevents further movement ofthe weight 240. As described above, engagement of gear teeth 248, 252and 256 with the non-rotating teeth 206 maintains weight 240 in anupright position and prevents the weight 240 from tipping, spinning orotherwise becoming misaligned within angled recesses 204 and 214. Afterrotation begins, centrifugal forces further push the weight 240 awayfrom the center of rotation of the flywheel 17. However, bottom edge 260prevents weight 240 from dislodging from the flywheel 17. The placementof weight 240 near the opening of receptacle 106 creates a center ofgravity similar to that observed with the insertion of a cassette 17.The flywheel 106 is therefore automatically balanced regardless of whichof the housings 200 have cassettes inserted into them.

In this regard, if cassettes 17 are inserted into each housing 200, thenthe moments exerted on the flywheel 105 by the housings 200, includingthe cassettes 17 and the weights 240 (which are all pushed close to thecenter of the flywheel 105 as described above), are evenly distributedsuch that the flywheel 105 is balanced, and the flywheel should smoothlyrotate without wobbling or other perturbations. If a cassette 17 isremoved from any housing 200, then the weight 240 for such housing 200automatically moves from near the center of the flywheel 105 to aposition further from such center until the gears 246, 250 and 254 restagainst the bottom edge 260 of angled recesses 204, 214, as describedabove. The mass of the weight 240 is selected so that the moment exertedon the flywheel 240 by such housing 200, which is missing a cassette 17,is substantially equal to the moment exerted on the flywheel 240 byanother housing 200 into which a cassette 17 is inserted. That is,moving a weight 240 further from the center of the flywheel increasesthe moment induced by the weight 240 thereby accommodating the removedcassette 17. Thus, the moments exerted by all of the housings 200 on theflywheel 105 are substantially equal and evenly distributed about theflywheel 105 so that the flywheel 105 remains balanced and does notwobble or experience other perturbations during rotation regardless ofwhich of the housings 200 actually have cassettes 17 inserted into them.

FIG. 17 depicts the flywheel 105 of FIG. 12 . The flywheel 105 has aplurality of microarray openings 130 extending vertically through theflywheel 105. A microarray of a cassette 17 may be aligned with eachopening 130 in order to allow the optics assembly 97 positioned belowthe flywheel 105 to capture data indicative of target agents detected bythe microarray of each cassette 17. In one embodiment, the flywheel 105has four microarray openings 130 corresponding to four receptacles 106(FIG. 12 ), but any number of receptacles 106 and openings 130 ispossible in other embodiments.

The flywheel 105 also has a center opening 131 for receiving a flywheelshaft (not shown). The flywheel 105 is coupled to the flywheel shaft viathe opening 131, and the flywheel shaft extends vertically in order tocouple the flywheel 105 to the large sheave 100 (FIG. 12 ) of the driveassembly 95 (FIG. 12 ). The flywheel 105 is rotated by the driveassembly 95 via the shaft.

FIG. 18 depicts a bottom perspective view of the flywheel 105 of FIG. 17. In one embodiment, the flywheel 105 comprises a rim 135 extending 360degrees around the center opening 131 on a bottom surface of theflywheel 105. The rim 135 indicates the orientation of the flywheel 105such that the control element 109 (FIG. 12 ) and the control element 15(FIG. 2 ) may know which cassette 17 corresponds to which microarraydata. As an example, in one embodiment, the rim 135 has three small gaps137 and a large gap 138, but other numbers of gaps 137 are possible inother embodiments.

A sensor (not shown) is coupled to the control element 109 and detectsthe gaps 137 and 138 in the rim 135. In one embodiment, the sensorcomprises a proximity sensor that detects the rim 135, although othertypes of sensors are possible in other embodiments. When the sensordetects a gap 137 or 138 in the rim, the sensor transmits a signal tothe control element 109 indicative of the size of the gap 137 or 138. Asthe flywheel 105 spins rapidly, the sensor repeatedly transmits signalsto the control element 109 indicating the sizes of the gaps 137 and 138in the rim 135 thereby indicating the orientation of each cassette 17 onthe flywheel 105. In this regard, the control element 109 identifieseach cassette 17 by its relation to the large gap 138. The controlelement 109 associates each cassette 17 with its respective receptacle106 via a detection element (not shown) that detects an identifier ofthe cassette 17 in the receptacle 106, or through manual input of theidentifier by a user via the user input interface 26 (FIG. 2 ). Forexample, in one embodiment, the large gap 138 is vertically-aligned witha particular receptacle 106. The control element 109 associates thelarge gap 138 with the cassette 17 in such receptacle 106, and thecontrol element 109 identifies such cassette 17 as the first cassette 17and identifies all of the other cassettes 17 on the flywheel 105 bytheir distance in the sequence from the first cassette 17. Thus, whenthe control element 109 receives a signal from the sensor indicating thelarge gap 138 is detected, the control element 109 associates themicroarray data detected by the optics assembly 97 at such time with thefirst cassette 17. The control element 109 further associates subsequentmicroarray data corresponding to the small gaps 137 with its respectivecassette 17. Accordingly, the control element 109 may accuratelyassociate microarray data with the appropriate cassette 17 based on thecassette's location with respect to the large gap 138.

FIG. 19 depicts an exemplary embodiment of the optics assembly 97 ofFIG. 12 . The optics assembly 97 comprises an OCA 114 and a laser 115mounted to a mounting plate 116. The assembly 97 is slideably mounted tothe track 108 (FIG. 12 ) via a rail 140. FIG. 20 depicts an exemplarymicroarray 144 of a cassette 17 (FIG. 1 ). The microarray 144 comprisesa plurality of dots 145 oriented in a plurality of rows 146-149. Thedots 145 are pre-formed on the microarray 144, and each dot is composedof a different material. The DNA of particular target agents bond tocertain dots 145 if the target agents are present in the specimen. Theexemplary microarray 144 shown in FIG. 20 comprises four rows 146-149having four dots 145 each, but different numbers of rows 146-149, dots145, and dot patterns are possible in other embodiments. Movement of theoptics assembly 97 along the track 108 allows the optics assembly 97 todetect one dimension of the microarray 144, while rotation of theflywheel 105 (FIG. 12 ) allows the optics assembly 97 to detect anotherdimension of the microarray 144. In this regard, the optics assembly 97performs a raster scan wherein the optics assembly 97 is stationary andscans a row 146 of dots 145 in the microarray 144 with a laser as theflywheel 105 rotates. After at least one full rotation of the flywheel105, the optics assembly 97 slides horizontally in order to scan thenext row 147 of dots 145. The optics assembly 97 continues such processuntil every row 146-149 of the dots 145 has been scanned. Accordingly,simultaneously rotating the flywheel 105 and sliding the optics assembly97 along the track 108 allows the optics assembly 97 to capture dataindicative of the microarray 144 on each cassette 17 positioned upon theflywheel 105.

Referring again to FIG. 19 , the OCA 114 comprises a lens 117 attachedto a beam splitter cube 142, and the OCA 114 is configured to determinewhich DNA has bonded to the dot, based on which dots fluoresce whenilluminated by a laser beam, as described in more detail below. In thisregard, the laser 115 transmits a laser beam (not shown) into the OCA114 and the laser beam travels into the beam splitter cube 142. Aportion of the beam is reflected and exits the OCA 114 via the lens 117.In one embodiment, a mirror (not shown) is positioned within the beamsplitter cube 142 and redirects the laser beam out the lens 117, butother methods of reflecting the beam within the cube 142 are possible.The laser beam is transmitted to the microarray 144 on the cassette 17and causes amplified DNA attached to the dots 145 of the microarray 144to fluoresce. Fluorescent dots 145 correspond to target agents thearm-PCR process is designed to detect. In this regard, the arm-PCRprocess amplifies DNA corresponding to particular target agents. Theamplified DNA for a particular target agent attaches to a particular dot145 in the microarray 144 and causes the dot 145 to fluoresce when it isexposed to a laser beam. The fluorescent dots 145 are detected by alight detection element 143 via the lens 117. In one embodiment, thelight detection element 143 comprises a photomultiplier tube (PMT), butdifferent types of light detection elements 143 are possible in otherembodiments. For example, in one embodiment, a high-sensitivity cameramay be used to capture an image of the microarray on each cassette 17within the reader 14.

As the optics assembly 97 moves along the track 108, each dot 145 in themicroarray 145 is detected for fluorescence. If the light detectionelement 143 detects a fluorescent dot 145, the control logic 32 (FIG. 2) marks the dot 145 in the test data 34 (FIG. 2 ). The control logic 32does so for each dot 145 in the microarray 144 such that all of thefluorescent dots 145 corresponding to detected target agents are markedin the test data 34. The control logic 32 compares the test data 34indicative of the fluorescent dots 145 to the predefined data 35 (FIG. 2) and transmits results of such comparison to a user via the user outputinterface 28 (FIG. 2 ), as set forth above. Accordingly, the user maydiagnose the specimen based on a comparison of the test data 34 to thepredefined data 35.

FIG. 21 depicts an exploded view of the OCA 114 of FIG. 19 . The OCA 114comprises the beam splitter cube 142, the lens 117, an input member 150,and a light detection member 151. The input member 150 is positioned ona side of the OCA 114 and is oriented towards the laser 115 (FIG. 19 ).The input member 150 receives the laser beam from the laser 115 andallows the beam to pass into the beam splitter cube 142. A beam splitter152 is positioned within the cube 142, and the beam splitter 152 isconfigured to redirect a portion of the laser beam towards the lens 117.The lens 117 is positioned on the top of the OCA 114, and the lens 117focuses the portion of the laser beam received from the beam splitter152 onto the microarray 144 (FIG. 20 ) in order to fluoresce the dots145 of the microarray 144 to which amplified DNA is attached.Fluorescent light from the dots 145 travels back into the lens 117,through the cube 142, and out of the OCA 114 via the light detectionmember 151.

The light detection member 151 is positioned on the bottom of the OCA114 and is coupled to the light detection element 143 (FIG. 19 ) via asleeve 155. The light detection member 151 allows fluorescent light fromthe microarray 144 to pass to the light detection element 143 fortransmission to the control element 109. The OCA 114 further comprises abeam dump member 156. The beam dump member 156 is configured to receivea portion of the laser beam which is not reflected through the lens 117and to dump the laser beam. The OCA 114 redirects the laser beam fromthe laser 115 and captures fluorescent light from dots 145 of themicroarray 144 which fluoresce due to exposure to the laser beam. Dataindicative of which dots fluoresce is transmitted to the control element15 for comparison to the predefined data 35.

FIG. 22 depicts an exemplary embodiment of an open platform targetsolution system 170. The system 170 comprises at least one communicationapparatus 172 coupled to a server 175 via a network 176. In oneembodiment, the server 175 hosts at least one web page 180 and comprisesprimer selection logic 182, primer data 183, target testing logic 185,and target solution data 186. A user, such as, for example, a targetsolution developer, may utilize the communication apparatus 172 toaccess the web page 180 in order to determine primers to use to detect aspecific target agent. In this regard, the user desires to detect anunregulated target agent using the open platform system for performingPCR amplification. The communication apparatus 172 communicates with theserver 175 via the network 176, such as, for example, the Internet, inorder to determine the appropriate primers for a given target agent. Inone embodiment, the user inputs a gene sequence for the target agentinto the web page 180. Based upon the input gene sequence, the primerselection logic 182 accesses the primer data 183 and identifies at leastone set of primers for detecting the target agent. In this regard, theprimer data 183 correlates various primers with specific gene sequences.The primer selection logic 182 displays suggested primers to the uservia the web page 180.

Based upon the suggested primers from the server 175, the user mayinsert such primers into the cassette 17 (FIG. 1 ) and perform an openplatform test on a specimen by selecting a set of settings (e.g., highspecificity, high sensitivity, or nominal) from the predefined settings32 (FIG. 2 ), as set forth above. The user may perform as many tests asdesired on the specimen using a variety of combinations of primerssuggested by the primer selection logic 182 and a variety of differentsets of settings 32 until a successful test is identified. In thisregard, different combinations of primers and settings 32 may produceresults having varying degrees of reliability in detecting the targetagent. Once the user determines a test that is a reliable combination ofprimers and settings for detecting the target agent, the user hasidentified a solution for that target agent (e.g., a “target solution”).

Upon determining a target solution, the user may again access the server175 via the web page 180 in order to submit his target solution to theserver 175. In this regard, the user may present his combination ofprimers and settings for the target agent to the server 175 as asolution for detecting the target agent, and the user may offer hiscombination to third party users interested in obtaining a solution forthe target agent. To do this, the user accesses the server 175 via theweb page 180, and the user indicates that he has determined a solutionfor the target agent. The user then manually inputs the target agent,the primers, and an input identifying the set of settings from thepredefined settings 32 that were used in the target solution. In oneembodiment, a server administrator may verify the target solution byperforming the test defined by the target solution in order to ensurethat the target solution is valid. However, other methods for validatingthe target solution are possible in other embodiments.

The target testing logic 185 provides the user with the opportunity tostore the target solution in the target solution data 186. The targetsolution data 186 indicates primers and settings 32 for various targetagents. Thus, if the user chooses to store the target solution in thetarget solution data 186, the target solution is available to thirdparty users. In one embodiment, the user may offer the target solutionfor sale to third party users. In this regard, once the target solutionis stored in the target solution data 186, a third party user (e.g.,“end user”) accesses the server 175 via another communication apparatus172. The end user may then browse the target solution data 186 via theweb page 180 in order to identify target solutions for a target agent hedesires to detect.

Upon identifying a desirable target solution, the end user may thenpurchase or otherwise obtain the target solution from the server 175. Inthis regard, in one embodiment, the end user may provide an indicationvia the web page 180 that he wishes to purchase a particular targetsolution for a given target agent. The server administrator or the userwho developed the target solution may then ship one or more cassettes 17configured to perform the target solution to the end user. For example,such cassettes 17 may contain the proper primers for detecting thetarget solution and may have an identifier (e.g., a bar code) on eachcassette 17, and the server administrator may update the ID mapping data33 to map such identifier to the appropriate set of predefined settings32 and predefined data 35 for the desired target solution. Thus, the enduser receives one or more cassettes 17 configured for detecting thetarget solution without learning which specific primers and set ofsettings 32 are used in the target solution. In this regard, the system10 may provide an indication whether the target agent is in the specimenunder test without the end user realizing the details of the test. Inother embodiments, the information (e.g., the primers and set ofsettings 32) about the target solution may be provided directly to theend user, if desired.

FIG. 28 depicts an exemplary embodiment of a cassette 17. Referring FIG.28 , the cassette has a pipette 220 that is operably connected to arotatable cam bar 216 so that rotation of the bar 216 results in acorresponding movement of the pipette 220 upward and/or downward in avertical direction. A pipette holder 228 supports and guides the up anddown movement of the cassette pipette 220, the pipette holder 228 beingsupported by and slidably positioned within the cassette 17. A leadscrew 224 is positioned within the cassette 17 is operably connected tothe pipette holder 228 so that rotation of the lead screw 224 produces acorresponding lateral movement of the pipette holder 228, therebyforming a means for positioning the pipette 220 above the appropriatefluid well 249 at each stage of the amplification/detection process.

The base 204 of the cassette 17 comprises at least one sample chamber242, and at least one reagent chamber 249 for containment of reagents(not shown). Reagent chamber 249 may be of identical, similar, ordissimilar size, shape, and depth and may be arranged in a variety ofpositions in the base 204 of the cassette 17. Desired reagents (notshown) are placed within the appropriate reagent chambers 249 so thatthe cassette pipette 220 may gather the reagents needed for theextraction and the two-step, two-primer-set amplification as the processproceeds within the cassette 17. Reagent chambers 249 may be pre-loadedand preferably sealed prior to shipping, with the sealing materialcomprising a material that will remain in place during shipping andstorage but be readily punctured by the force of downward motion of thecassette pipette in order to open the reagent chamber 249 to allowretrieval of the contents using the cassette pipette 220. One suchmaterial that is appropriate for sealing the reagent chamber, eitherindividually, or as a group, is a thin sheet of aluminum foil (notshown). In aspects of the disclosure, among the reagent chambers are tworeagent chambers which will contain target-specific primers and common,non-target-specific primers, respectively. These primers are used forthe first and second amplification reactions, the first amplificationbeing target-specific to provide amplicons representing the DNA and/orRNA of the variety of targets which may be found within the sample, andthe second amplification being primed by common primers to allowsemi-quantitative non-specific amplification of the amplicons of thefirst amplification. In this two-step process, the first amplificationbeing primed by target-specific primers provides specificity, while thesecond amplification being primed by common primers increasessensitivity.

Also provided in the base 204 of the cassette 17 is a detection chamber248 containing a microarray 244 for detection of the DNA which has beenamplified during the two-step ARM-PCR protocol. Microarrays are known inthe art and methods for preparing target-specific microarrays arewell-known to those of skill in the art.

A fill port 214 in the top of the cassette allows a user to insert apipette (not shown) from the environment outside the cassette into asample chamber 242. A clear plastic window (not shown) may be formed inthe cassette 17 to be position so that it allows the user to see theuser's pipette tip (not shown) as it is being inserted into the cassette17 to deposit the sample (not shown) to be analyzed. In one embodiment,the clear viewing window is constructed to withstand the temperatureextremes of the cassette. Alternatively, the entire enclosure of thecassette 17 may be formed from transparent or translucent plasticsallowing the user to visualize the inner workings of the cassette 17.

In one embodiment, the fill port cap 212 located on top of the cassettewill be a one-time operation cap, meaning that once the cap is sealedafter sample insertion it cannot be reopened, thereby maintaining theintegrity of the seal and keeping the system closed. In anotherembodiment, a sliding door 210 may be utilized such that once the sample(not shown) is introduced into the cassette 17, the sliding door 210 maybe slid and locked into place. The fill port cap 212 seals the fill port214. In one embodiment, the fill port 214 has a minimum inside diameterof 0.3 inches to allow for insertion of a 20 μl pipette through the fillport 214 and into the sample chamber 242. The fill port 214 may be othersizes in other embodiments of the present disclosure.

Movement of the cassette pipette 220 in a vertical, up-and-down manner,is provided by a cam bar 216 which is connected to a processor module 40by means of a mechanical interface 218 immovably coupled to the cam bar216, allowing movement of the cassette pipette 220 to be controlled bythe processor module 4. In one embodiment, the mechanical interface 18is a knob, however, other mechanical interfaces may be used in otherembodiments.

The cassette pipette 220 is supported and held in position by a pipetteholder 228. The pipette holder 228 is slidably received along the lengthof the cassette 17. The pipette holder 228 may be retained along thesame lateral plane of the cassette 17 by a first and second guiderail(not shown) which can be molded into the sides of the cassette 1. Suchguiderails may be positioned vertically parallel to each other andhorizontally positioned between the ends of the cassette 17. The pipetteholder 228 is operably connected to the lead screw 224. The lead screw224 is threadedly received into the pipette holder 228 by means of amale-female thread pairing between the lead screw 224 and the pipetteholder 228. A mechanical interface 240 is immovably connected to thelead screw 224 allowing both clockwise and counterclockwise rotation.Rotation of the mechanical interface 240 rotates the lead screw 224, thepipette holder 228 follows the thread of the lead screw 224 and is movedlaterally along the lead screw 224 along the length of the cassette 17.Reversing the direction of rotation of the lead screw 224 causes acorresponding reversal of motion of the pipette holder 228. Bycontrolling the number of rotations and direction of rotation of thelead screw 228, the pipette can be accurately positioned above any oneof the reagent chamber 249 or sample chamber 242 located in the base204. In one embodiment, the mechanical interface 240 is a knob, however,other types of mechanical interfaces may be used in other embodiments.

It should be emphasized that the cassette 17 of FIGS. 28 and 29 isexemplary, and other types of cassettes may be used in otherembodiments.

Now, therefore, the following is claimed:
 1. A system comprising: areader comprising: a flywheel, the flywheel having at e t one indicatorto indicate an orientation of the flywheel; a motor coupled to theflywheel to rotate the flywheel; a plurality of receptacles positionedon a first surface of the flywheel, each receptacle of the plurality ofreceptacles configured to receive a cassette containing a microarraywith a nucleic acid sample; a sensor configured to detect the at leastone indicator of the flywheel; a processor coupled to the sensor toreceive a signal indicative of detection of the at least one indicator,the processor configured to identify a receptacle of the plurality ofreceptacles using the received signal from the sensor, the processorfurther configured to associate each receptacle of the plurality ofreceptacles with a corresponding cassette in the receptacle; an opticsassembly coupled to the processor, the optics assembly configured tocapture test data from the microarray of a cassette positioned in areceptacle of the plurality of receptacles, wherein the optics assemblycomprises a laser and a light detection element, the light detectionelement configured to detect dots in the microarray that fluoresce inresponse to being exposed to the laser, wherein the test datacorresponds to data on which dots fluoresced; and the processor furtherconfigured to receive the test data from the optics assembly and toassociate the received test data with a cassette based on anidentification of the receptacle for the cassette using the receivedsignal from the sensor; and a computing device in communication with theprocessor of the reader to receive the test data for a microarray of acassette, the computing device configured to analyze the test data andprovide an output indicative of a comparison of the test data topredefined data.
 2. The system of claim 1, wherein the plurality ofreceptacles includes four receptacles positioned perpendicularly to oneanother.
 3. A system comprising: a reader comprising: a flywheel, theflywheel having at least one indicator to indicate an orientation of theflywheel; a motor coupled to the flywheel to rotate the flywheel; aplurality of receptacles positioned on a first surface of the flywheel,each receptacle of the plurality of receptacles configured to receive acassette containing a microarray with a nucleic acid sample: a sensorconfigured to detect the at least one indicator of the flywheel; aprocessor coupled to the sensor to receive a signal indicative ofdetection of the at least one indicator, the processor configured toidentify a receptacle of the plurality of receptacles using the receivedsignal from the sensor, the processor further configured to associateeach receptacle of the plurality of receptacles with a correspondingcassette in the receptacle; an optics assembly coupled to the processor,the optics assembly configured to capture test data from the microarrayof a cassette positioned in a receptacle of the plurality ofreceptacles; and the processor further configured to receive the testdata from the optics assembly and to associate the received test datawith a cassette based on an identification of the receptacle for thecassette using the received signal from the sensor; and a computingdevice in communication with the processor of the reader to receive thetest data for a microarray of a cassette, the computing deviceconfigured to analyze the test data and provide an output indicative ofa comparison of the test data to predefined data, wherein the flywheelcomprises a rim located on a second surface of the flywheel opposite thefirst surface, and wherein the at least one indicator forms at least onegap in the rim.
 4. A system comprising: a reader comprising: a flywheel,the flywheel having at least one indicator to indicate an orientation ofthe flywheel; a motor coupled to the flywheel to rotate the flywheel; aplurality of receptacles positioned on a first surface of the flywheel,each receptacle of the plurality of receptacles configured to receive acassette containing a microarray with a nucleic acid sample; a sensorconfigured to detect the at least one indicator of the flywheel; aprocessor coupled to the sensor to receive a signal indicative ofdetection of the at least one indicator, the processor configured toidentify a receptacle of the plurality of receptacles using the receivedsignal from the sensor, the processor further configured to associateeach receptacle of the plurality of receptacles with a correspondingcassette in the receptacle; an optics assembly coupled to the processor,the optics assembly configured to capture test data from the microarrayof a cassette positioned in a receptacle of the plurality ofreceptacles; and the processor further configured to receive the testdata from the optics assembly and to associate the received test datawith a cassette based on an identification of the receptacle for thecassette using the received signal from the sensor; and a computingdevice in communication with the processor of the reader to receive thetest data for a microarray of a cassette, the computing deviceconfigured to analyze the test data and provide an output indicative ofa comparison of the test data to predefined data, wherein the flywheelcomprises a rim located on a second surface of the flywheel opposite thefirst surface, and wherein the rim includes the at least one indicator.5. The system of claim 4, wherein the at least one indicator has aplurality of gaps in the rim, wherein each gap corresponds to areceptacle of the plurality of receptacles.
 6. The system of claim 5,wherein the plurality of gaps includes a first gap and a plurality ofsecond gaps, wherein the first gap is larger than each of the secondgaps, and wherein each receptacle is identified relative to thedetection of the first gap by the sensor.
 7. A system comprising: areader comprising: a flywheel, the flywheel having at least oneindicator to indicate an orientation of the flywheel; a motor coupled tothe flywheel to rotate the flywheel; a plurality of receptaclespositioned on a first surface of the flywheel, each receptacle of theplurality of receptacles configured to receive a cassette containing amicroarray with a nucleic acid sample; a sensor configured to detect theat least one indicator of the flywheel; a processor coupled to thesensor to receive a signal indicative of detection of the at least oneindicator, the processor configured to identify a receptacle of theplurality of receptacles using the received signal from the sensor, theprocessor further configured to associate each receptacle of theplurality of receptacles with a corresponding cassette in thereceptacle; an optics assembly coupled to the processor, the opticsassembly configured to capture test data from the microarray of acassette positioned in a receptacle of the plurality of receptacles,wherein the optics assembly comprises a laser and a light detectionelement, the light detection element configured to detect dots in themicroarray that fluoresce in response to being exposed to the laser,wherein the test data corresponds to data on which dots fluoresced; andthe processor further configured to receive the test data from theoptics assembly and to associate the received test data with a cassettebased on an identification of the receptacle for the cassette using thereceived signal from the sensor; and a computing device in communicationwith the processor of the reader to receive the test data for amicroarray of a cassette, the computing device configured to analyze thetest data and provide an output indicative of a comparison of the testdata to predefined data, wherein the flywheel has a plurality ofopenings, wherein each opening of the plurality of openings correspondsto a receptacle of the plurality of receptacles, and wherein eachopening permits the optics assembly to capture test data from amicroarray of a corresponding cassette located in the receptacle.
 8. Asystem comprising: a reader comprising: a flywheel, the flywheel havingat least one indicator to indicate an orientation of the flywheel; amotor coupled to the flywheel to rotate the flywheel; a plurality ofreceptacles positioned on a first surface of the flywheel, eachreceptacle of the plurality of receptacles configured to receive acassette containing a microarray with a nucleic acid sample, whereineach receptacle of the plurality of receptacles comprises a balancedevice configured to automatically balance the flywheel, and wherein thebalance device compensates for the absence of a cassette in areceptacle; a sensor configured to detect the at least one indicator ofthe flywheel; a processor coupled to the sensor to receive a signalindicative of detection of the at least one indicator, the processorconfigured to identify a receptacle of the plurality of receptaclesusing the received signal from the sensor, the processor furtherconfigured to associate each receptacle of the plurality of receptacleswith a corresponding cassette in the receptacle; an optics assemblycoupled to the processor, the optics assembly configured to capture testdata from the microarray of a cassette positioned in a receptacle of theplurality of receptacles; and the processor further configured toreceive the test data from the optics assembly and to associate thereceived test data with a cassette based on an identification of thereceptacle for the cassette using the received signal from the sensor;and a computing device in communication with the processor of the readerto receive the test data for a microarray of a cassette, the computingdevice configured to analyze the test data and provide an outputindicative of a comparison of the test data to predefined data.
 9. Thesystem of claim 8, wherein the balance device comprises a weightconfigured to move from a first end of the receptacle near a center ofthe flywheel to a second end of the receptacle near an edge of theflywheel.
 10. The system of claim 9, wherein the weight is configured toautomatically move from the first end of the receptacle to the secondend of the receptacle upon removal of a cassette from the receptacle.11. A method comprising: inserting a cassette containing a microarraywith a nucleic acid sample into a receptacle of a plurality ofreceptacles positioned on a first surface of a flywheel; rotating theflywheel with a motor; sensing, with a sensor while the flywheel isrotating, at least one indicator associated with the flywheel, the atleast one indicator for indicating an orientation of the flywheel;receiving, by a processor, a signal from the sensor indicative ofdetection of the at least one indicator; identifying, while the flywheelis rotating, a receptacle of the plurality of receptacles with theprocessor using the received signal; associating; by the processor, eachreceptacle of the plurality of receptacles with a corresponding cassettein the receptacle; capturing, while the flywheel is rotating, test datafrom the microarray of the cassette with an optics assembly, wherein theoptics assembly comprises a laser and a light detection element;exposing dots in the microarray to light from the laser; detecting, withthe light detection element, the dots in the microarray that fluorescein response to being exposed to light from the laser, wherein the testdata corresponds to data relating to the detection of which dotsfluoresced; providing, by the optics assembly, the test data to theprocessor; associating, by the processor, the test data with a cassettebased on an identification of the receptacle for the cassette using thereceived signal from the sensor; receiving, by a computing device, thetest data for a microarray of a cassette from the processor; andanalyzing, by the computing device, the test data and providing anoutput indicative of a comparison of the test data to predefined data.12. A method comprising: inserting a cassette containing a microarraywith a nucleic add sample into a receptacle of a plurality ofreceptacles positioned on a first surface of a flywheel; rotating theflywheel with a motor; sensing, with a sensor while the flywheel isrotating, at least one indicator associated with the flywheel, the atleast one indicator for indicating an orientation of the flywheel,wherein the at least one indicator forms a gap in a rim of the flywheel;receiving, by a processor, a signal from the sensor indicative ofdetection of the at least one indicator; identifying, while the flywheelis rotating, a receptacle of the plurality of receptacles with theprocessor using the received signal; associating, by the processor, eachreceptacle of the plurality of receptacles with a corresponding cassettein the receptacle; capturing while the flywheel is rotating, test datafrom the microarray of the cassette with an optics assembly; providing,by the optics assembly, the test data to the processor; associating, bythe processor, the test data with a cassette based on an identificationof the receptacle for the cassette using the received signal from thesensor; receiving, by a computing device, the test data for a microarrayof a cassette from the processor; and analyzing, by the computingdevice, the test data and providing an output indicative of a comparisonof the test data to predefined data.
 13. A method comprising: insertinga cassette containing a microarray with a nucleic add sample into areceptacle of a plurality of receptacles positioned on a first surfaceof a flywheel; rotating the flywheel with a motor; sensing, with asensor while the flywheel is rotating, at least one indicator associatedwith the flywheel, the at least one indicator for indicating anorientation of the flywheel, wherein the sensing the at least oneindicator includes sensing the at least one indicator at a rim of theflywheel on a second surface of the flywheel opposite the first surface;receiving, by a processor, a signal from the sensor indicative ofdetection of the at least one indicator; identifying, while the flywheelis rotating, a receptacle of the plurality of receptacles with theprocessor using the received signal; associating, by the processor, eachreceptacle of the plurality of receptacles with a corresponding cassettein the receptacle; capturing, while the flywheel is rotating, test datafrom the microarray of the cassette with an optics assembly; providing,by the optics assembly, the test data to the processor; associating, bythe processor, the test data with a cassette based on an identificationof the receptacle for the cassette using the received signal from thesensor; receiving, by a computing device, the test data for a microarrayof a cassette from the processor; and analyzing, by the computingdevice, the test data and providing an output indicative of a comparisonof the test data to predefined data.
 14. The method of claim 13, whereinthe at least one indicator has a plurality of gaps in the rim, whereineach gap corresponds to a receptacle of the plurality of receptacles.15. The method of claim 14, wherein the plurality of gaps includes afirst gap and a plurality of second gaps, wherein the first gap islarger than each of the second gaps, and wherein the identifying thereceptacle includes identifying the receptacle relative to the sensingof the first gap.
 16. A method comprising: inserting a cassettecontaining a microarray with a nucleic acid sample into a receptacle ofa plurality of receptacles positioned on a first surface of a flywheel;rotating the flywheel with a motor; sensing, with a sensor while theflywheel is rotating, at least one indicator associated with theflywheel, the at least one indicator for indicating an orientation ofthe flywheel; receiving, by a processor, a signal from the sensorindicative of detection of the at least one indicator; identifying,while the flywheel is rotating, a receptacle of the plurality ofreceptacles with the processor using the received signal; associating,by the processor, each receptacle of the plurality of receptacles with acorresponding cassette in the receptacle; capturing, while the flywheelis rotating, test data from the microarray of the cassette with anoptics assembly; providing, by the optics assembly, the test data to theprocessor; associating, by the processor, the test data with a cassettebased on an identification of the receptacle for the cassette using thereceived signal from the sensor; receiving, by a computing device, thetest data for a microarray of a cassette from the processor; analyzing,by the computing device, the test data and providing an outputindicative of a comparison of the test data to predefined data; andsliding the optics assembly along a track, while the flywheel isrotating, to scan the microarray.
 17. A method comprising: inserting acassette containing a microarray with a nucleic acid sample into areceptacle of a plurality of receptacles positioned on a first surfaceof a flywheel, wherein the flywheel comprises has a plurality ofopenings, and wherein each opening of the plurality of openingscorresponds to a receptacle of the plurality of receptacles; rotatingthe flywheel with a motor; sensing, with a sensor while the flywheel isrotating, at least one indicator associated with the flywheel, the atleast one indicator for indicating an orientation of the flywheel;receiving, by a processor, a signal from the sensor indicative ofdetection of the at least one indicator; identifying, while the flywheelis rotating, a receptacle of the plurality of receptacles with theprocessor using the received signal; associating, by the processor, eachreceptacle of the plurality of receptacles with a corresponding cassettein the receptacle; capturing, while the flywheel is rotating, test datafrom the microarray of the cassette with an optics assembly via theopening located in the corresponding receptacle for the cassette;providing, by the optics assembly, the test data to the processor;associating, by the processor, the test data with a cassette based on anidentification of the receptacle for the cassette using the receivedsignal from the sensor; receiving, by a computing device, the test datafor a microarray of a cassette from the processor; and analyzing, by thecomputing device, the test data and providing an output indicative of acomparison of the test data to predefined data.
 18. A method comprising:inserting a cassette containing a microarray with a nucleic acid sampleinto a receptacle of a plurality of receptacles positioned on a firstsurface of a flywheel; rotating the flywheel with a motor; sensing, witha sensor while the flywheel is rotating, at least one indicatorassociated with the flywheel, the at least one indicator for indicatingan orientation of the flywheel; receiving, by a processor, a signal fromthe sensor indicative of detection of the at least one indicator;identifying, while the flywheel is rotating, a receptacle of theplurality of receptacles with the processor using the received signal;associating, by the processor, each receptacle of the plurality ofreceptacles with a corresponding cassette in the receptacle; capturing,while the flywheel is rotating; test data from the microarray of thecassette with an optics assembly; providing, by the optics assembly, thetest data to the processor; associating, by the processor, the test datawith a cassette based on an identification of the receptacle for thecassette using the received signal from the sensor; receiving, by acomputing device, the test data for a microarray of a cassette from theprocessor; analyzing, by the computing device, the test data andproviding an output indicative of a comparison of the test data topredefined data; and compensating for the absence of the cassette in thereceptacle with a balance device configured to automatically balance theflywheel.
 19. The method of claim 18, wherein compensating for theabsence of a cassette in the receptacle includes moving a weight from afirst end of the receptacle near a center of the flywheel to a secondend of the receptacle near an edge of the flywheel.
 20. The method ofclaim 19, wherein the moving the weight includes automatically movingthe weight from the first end of the receptacle to the second end of thereceptacle upon removal of a cassette from the receptacle.